A friend of mine did this exact swap, an I'm in the middle of it right now.. Ther's a few details on the swap, but it's pretty much just like throwing another 2v in there. So here we go.....
Since youre car's an auto, you will need an 5sp GT ECU to run the T-45, or use the Cobra W-Harness/ECU (If you have), but you'll have to get an Cobra gauge cluster key & tumbler to avoid all the PATS issues (or just get a HH tuner to deal w/it)
So using the GT wiring an computer which simplify's it, you will need to lengthen the IAC, TPS, an Coolant temp, sens/switch. Some guy's had to some did'nt, weird... Re-use the GT MAF an 19lb injectors untill you get a tune to run the 24's an 80mm Cobra MAF
If you want youre speedo an reverse light to function you'll need the 5 speed tunnel wiring also. An the coolant hoses an thermostat housing can be pricey an hard to find sometime's also. An the throttle cable

make sure you grab that off the Cobra, so hard to find now an are$$
Youre GT H-pipe should bolt right up, an the rear end's are pretty much identical.
An if you use the GT ECU, you'll have to pull the IMRC"s an delete the butterfly's, unless you want to rig up a window switch or something to keep them.
Pretty sure I covered all the bases on the swap, I decided to go the budget Mark VIII route, and am still hunting down pieces here an there. Pretty sure I covered all bases on the swap, so good luck bro! Happy Motoring People's ! ! !